Then you put it somewhere that it can't be easily accessed by the unknowing. Which, IIRC, was already the case--there's no menu option for "chrome://plugins".

Making idiot-proofing your top design priority "for the user's own good" is a really bad idea that invariably results in a less functional product for no substantial benefit. If people are getting confused and messing with things they didn't mean to, the solution is better interface design, not axing useful features.